Duplicate transactions in undeposited funds

I am a relatively new business owner, and have been managing the books myself. I own a small wine shop, running Square as a POS, and have the transactions automatically imported into QBO. A (real) bookkeeper helped me at the beginning with the workflow of matching the deposits and bill payments, and I have been reconciling the credit card and bank accounts every month with few issues. The undeposited funds account seemed to be humming along correctly as I matched transactions daily, so I sort of forgot about it. 

However, I was recently poking around in the chart of accounts and realized it had been off by about $1600 for some time. I did some digging and found the biggest culprit was a duplicate sales receipt for $1392.92 that did not have an R in the bank feed column. I have hesitant to delete it, because I'm not really sure what the ramifications will be- there is no such duplicate in the bank account, but that month has been reconciled, and since my bookkeeping experience is pretty limited, I'm afraid of making an even bigger mess. Any suggestions?